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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1529/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PharmacoGx 3.11.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/PharmacoGx
git_branch: devel
git_last_commit: 18017f6
git_last_commit_date: 2024-10-29 10:13:25 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for PharmacoGx on kunpeng2

To the developers/maintainers of the PharmacoGx package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PharmacoGx.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PharmacoGx
Version: 3.11.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PharmacoGx_3.11.0.tar.gz
StartedAt: 2024-12-24 09:47:22 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:55:13 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 470.7 seconds
RetCode: 0
Status:   OK  
CheckDir: PharmacoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PharmacoGx_3.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PharmacoGx’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ...Warning: program compiled against libxml 212 using older 211
 OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.Hill’ ‘.summarizeSensitivityNumbers’ ‘partialCorQUICKSTOP’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeZIPdelta: no visible binding for global variable
  ‘EC50_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable
  ‘EC50_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘HS_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable
  ‘HS_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘E_inf_proj_2_to_1’
.computeZIPdelta: no visible binding for global variable
  ‘E_inf_proj_1_to_2’
.computeZIPdelta: no visible binding for global variable ‘Rsqr_1_to_2’
.computeZIPdelta: no visible binding for global variable ‘Rsqr_2_to_1’
.plotProjHill: no visible binding for global variable ‘treatment1id’
.plotProjHill: no visible binding for global variable ‘treatment2id’
.plotProjHill: no visible binding for global variable ‘treatment2dose’
.plotProjHill: no visible binding for global variable
  ‘EC50_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘HS_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘EC50_2’
.plotProjHill: no visible binding for global variable ‘E_inf_2’
.plotProjHill: no visible binding for global variable
  ‘E_inf_proj_2_to_1’
.plotProjHill: no visible binding for global variable ‘HS_2’
.plotProjHill: no visible binding for global variable ‘treatment1dose’
.plotProjHill: no visible binding for global variable ‘combo_viability’
.plotProjHill: no visible binding for global variable ‘x’
.plotProjHill: no visible binding for global variable
  ‘EC50_proj_1_to_2’
.plotProjHill: no visible binding for global variable ‘HS_proj_1_to_2’
.plotProjHill: no visible binding for global variable ‘EC50_1’
.plotProjHill: no visible binding for global variable ‘HS_1’
.plotProjHill: no visible binding for global variable ‘E_inf_1’
.plotProjHill: no visible binding for global variable
  ‘E_inf_proj_1_to_2’
PharmacoSet2: no visible global function definition for
  ‘MultiAssayExperiment’
fitTwowayZIP: no visible binding for global variable ‘treatment1dose’
fitTwowayZIP: no visible binding for global variable ‘combo_viability’
fitTwowayZIP: no visible binding for global variable ‘treatment2dose’
fitTwowayZIP: no visible binding for global variable ‘EC50_2’
fitTwowayZIP: no visible binding for global variable ‘HS_2’
fitTwowayZIP: no visible binding for global variable ‘E_inf_2’
fitTwowayZIP: no visible binding for global variable ‘EC50_1’
fitTwowayZIP: no visible binding for global variable ‘HS_1’
fitTwowayZIP: no visible binding for global variable ‘E_inf_1’
mergePSets: no visible global function definition for
  ‘checkPSetStructure’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘ZIP’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘EC50_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘HS_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_proj_2_to_1’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘E_inf_proj_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘treatment1dose’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘treatment2dose’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘Rsqr_1_to_2’
computeZIPdelta,TreatmentResponseExperiment: no visible binding for
  global variable ‘Rsqr_2_to_1’
Undefined global functions or variables:
  EC50_1 EC50_2 EC50_proj_1_to_2 EC50_proj_2_to_1 E_inf_1 E_inf_2
  E_inf_proj_1_to_2 E_inf_proj_2_to_1 HS_1 HS_2 HS_proj_1_to_2
  HS_proj_2_to_1 MultiAssayExperiment Rsqr_1_to_2 Rsqr_2_to_1 ZIP
  checkPSetStructure combo_viability treatment1dose treatment1id
  treatment2dose treatment2id x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  computeZIPdelta-TreatmentResponseExperiment-method.Rd:
    TreatmentResponseExperiment
  fitTwowayZIP.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.


Installation output

PharmacoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘PharmacoGx’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c metaPermC.c -o metaPermC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c rCPP_bridge.cpp -o rCPP_bridge.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-PharmacoGx/00new/PharmacoGx/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PharmacoGx)

Tests output

PharmacoGx.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.unsetenv("R_TESTS")
> 
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'PharmacoGx'

The following objects are masked from 'package:CoreGx':

    .parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc

> 
> test_check("PharmacoGx")

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[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

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[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_PharmacoSet_utils.R:28:1'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
 98.854   2.120 101.516 

Example timings

PharmacoGx.Rcheck/PharmacoGx-Ex.timings

nameusersystemelapsed
PharmacoSet-accessors3.0540.5873.650
PharmacoSet-utils1.7450.0081.756
PharmacoSet0.0020.0000.003
PharmacoSet22.0750.0122.092
PharmacoSig0.0400.0240.276
amcc0.0000.0010.001
availablePSets0.0000.0010.001
callingWaterfall000
checkPsetStructure1.2530.0401.296
computeABC1.1060.1591.269
computeAUC0.5880.0200.610
computeAmax0.5650.0200.587
computeBliss0.0010.0000.001
computeHSA000
computeICn1.0910.0081.102
computeLoewe0.0000.0000.001
computeSlope0.0000.0000.001
computeZIP0.0010.0000.001
computeZIPdelta-TreatmentResponseExperiment-method0.0000.0000.001
computeZIPdelta000
connectivityScore3.6850.1803.978
cosinePerm0.0920.0930.112
dot-computeZIPdelta000
downloadPSet000
downloadPertSig000
drugDoseResponseCurve000
drugPerturbationSig2.5630.3592.828
drugSensitivitySig-PharmacoSet-method1.4250.0511.480
effectToDose0.0000.0000.001
filterNoisyCurves1.5740.0721.651
fitTwowayZIP000
geneDrugSensitivity000
geneDrugSensitivityPBCorr000
geneDrugSensitivityPCorr000
gwc1.2050.0441.312
hillCurve0.0000.0000.001
intersectPSet1.4860.1251.517
loeweCI000
logLogisticRegression0.6060.1030.712
mcc0.0150.0272.593
plot.PharmacoSig4.0790.6682.161
show-PharmacoSet-method1.1820.0361.221
show-PharmacoSig-method1.4660.1071.575
showSigAnnot-PharmacoSig-method1.4060.1271.536
sub-PharmacoSet-ANY-ANY-ANY-method1.2730.0281.305
subsetTo-PharmacoSet-method1.2980.0121.311
summarizeMolecularProfiles-PharmacoSet-method0.1460.0040.151
summarizeSensitivityProfiles-PharmacoSet-method0.0620.0080.071
updateObject-PharmacoSet-method0.1200.0040.124